Commit 710f0b9c authored by Christer Ejsing's avatar Christer Ejsing
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README

parent 1feed786
# ALEX123 # ALEX123
## Description ALEX123 (Analysis of Lipid EXperiments, for processing FTMS, MS2 and MS3 data) is software framework for analyzing high resolution shotgun and MALDI-based lipidomics data.
ALEX123 (Analysis of Lipid EXperiments for processing FTMS, MS2 and MS3 data) is software framework for analyzing high resolution shotgun and MALDI-based lipidomics data.
+ The procedure for high confidence lipid identification using MALDI-based FTMS and ITMS2 data is described in Ellis et al. (2018, under review). A link to a user guide and an example dataset is provided below. + The procedure for high confidence lipid identification using MALDI-based FTMS and ITMS2 data is described in Ellis et al. (2018, under review). A link to a user guide and an example dataset is provided below.
## Requirements ## Requirements
+ The ALEX123 software framework is operational on desktop and labtop computers running Microsoft Windows 7 or 10 (Professional 64-bit), and having at least a 2.7 GHz dual core processor with at least 8 GB RAM. The user should have administrator rights. + The ALEX123 software framework is operational on desktop and labtop computers running Microsoft™ Windows™ 7 or 10 (Professional 64-bit), and having at least a 2.7 GHz dual core processor with at least 8 GB RAM. The user should have administrator rights.
+ Install Java (64-bit) to use Java-based ALEX123 software modules. + Install Java (64-bit) to use Java-based ALEX123 software modules.
+ Install MSFileReader (64-bit) (MSFileReader_x64_3.1 SP4.exe) (Thermo Fisher Scientific) to use the Python-based ALEX123 converter. + Install MSFileReader (64-bit) (”MSFileReader_x64_3.1 SP4.exe”) (Thermo Fisher Scientific) to use the Python-based ALEX123 converter.
+ Install Python 3.6.1 (64-bit) and comtypes to use the Python-based ALEX123 converter. **Click here for instructions.** + Install Python 3.6.1 (64-bit) and comtypes to use the Python-based ALEX123 converter. **Click here for instructions.**
+ Install SAS® 9.2 with SAS® Enterprise Guide 5.1 to use scripts (file extension .epg) for automated high confidence lipid identification. **More information is available here.** + Install SAS® 9.2 with SAS® Enterprise Guide 5.1 to use scripts (file extension .epg) for automated high confidence lipid identification. **More information is available here.**
+ Install Tableau® Desktop (version 10.2 or later) to use and modify data visualization templates (file extensions .twb). **More information is available here.** + Install Tableau® Desktop (version 10.2 or later) to use and modify data visualization templates (file extensions .twb). **More information is available here.**
## Example dataset for high confidence lipid identification using MALDI-based FTMS and ITMS2 data ## Example dataset for high confidence lipid identification using MALDI-based FTMS and ITMS2 data
...@@ -25,3 +23,4 @@ Click here to download the **user guide (.pdf).** ...@@ -25,3 +23,4 @@ Click here to download the **user guide (.pdf).**
Click here to download the **example dataset** (.zip, 93 MB). Click here to download the **example dataset** (.zip, 93 MB).
Note that mass spectrometry data files (.RAW) should be downloaded separately from the **MetaboLight repository (MTBLS597).** Note that mass spectrometry data files (.RAW) should be downloaded separately from the **MetaboLight repository (MTBLS597).**
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